Our long-term objective is to understand the complex network of genetic interactions that underlies the processes of normal development, disease and evolution. For this, we need to determine gene expression profiles for the full complement of genes in an organism. At the Berkeley Drosophila Genome Project (BDGP), we have established a gene expression resource for Drosophila development that contains spatial and temporal embryonic expression patterns as well as annotations of the patterns using a standardized, controlled vocabulary, based on Gene Ontology (GO). Our database currently contains 75,000 annotated images showing expression patterns generated using in-situ hybridization of staged whole-mounted embryos for approximately 45% (6,000) of the protein-coding genes in the Drosophila genome. The spatial expression data are integrated with our developmental microarray data. We propose to extend these studies to: (1) the remaining 55% of the protein-coding genes, (2) alternatively-spliced transcripts, and (3) non-coding RNA candidate genes The primary resource for generation of RNA probes is our Drosophila Gene Collection (DGC) which currently contains cDNA clones corresponding to 80% of the annotated genes. To capture expression patterns for genes that do not have a representative cDNA clone (20%), we used gene-specific PCR products to generate RNA probes in 96-well format. The gene expression data produced by our study will provide fundamental information for elaborating the function of the 13,664 genes in Drosophila and will aid in elucidating the function of the homologous genes in other eukaryotes, including humans. In addition, the integration of the gene expression data with gene, transcript and protein sequences will promote research to discover networks of regulatory interactions. Using the standardized vocabulary allows cross-species descriptions of gene expression and tissue differentiation. Elucidating the mechanisms responsible for genome-wide gene expression and regulation in Drosophila development will aid in understanding normal growth and differentiation of tissues in humans, prerequisites for understanding human disease.